Nestled in a back corner of Mogadishu's Aden Adde International Airport is a sprawling walled compound run by the Central Intelligence Agency. Set on the coast of the Indian Ocean, the facility looks like a small gated community, with more than a dozen buildings behind large protective walls and secured by guard towers at each of its four corners. Adjacent to the compound are eight large metal hangars, and the CIA has its own aircraft at the airport. The site, which airport officials and Somali intelligence sources say was completed four months ago, is guarded by Somali soldiers, but the Americans control access. At the facility, the CIA runs a counterterrorism training program for Somali intelligence agents and operatives aimed at building an indigenous strike force capable of snatch operations and targeted "combat" operations against members of Al Shabab, an Islamic militant group with close ties to Al Qaeda.

As part of its expanding counterterrorism program in Somalia, the CIA also uses a secret prison buried in the basement of Somalia's National Security Agency (NSA) headquarters, where prisoners suspected of being Shabab members or of having links to the group are held. Some of the prisoners have been snatched off the streets of Kenya and rendered by plane to Mogadishu. While the underground prison is officially run by the Somali NSA, US intelligence personnel pay the salaries of intelligence agents and also directly interrogate prisoners. The existence of both facilities and the CIA role was uncovered by The Nation during an extensive on-the-ground investigation in Mogadishu. Among the sources who provided information for this story are senior Somali intelligence officials; senior members of Somalia's Transitional Federal Government (TFG); former prisoners held at the underground prison; and several well-connected Somali analysts and militia leaders, some of whom have worked with US agents, including those from the CIA. A US official, who confirmed the existence of both sites, told The Nation, "It makes complete sense to have a strong counterterrorism partnership" with the Somali government.

The CIA presence in Mogadishu is part of Washington's intensifying counterterrorism focus on Somalia, which includes targeted strikes by US Special Operations forces, drone attacks and expanded surveillance operations. The US agents "are here full time," a senior Somali intelligence official told me. At times, he said, there are as many as thirty of them in Mogadishu, but he stressed that those working with the Somali NSA do not conduct operations; rather, they advise and train Somali agents. "In this environment, it's very tricky. They want to help us, but the situation is not allowing them to do [it] however they want. They are not in control of the politics, they are not in control of the security," he adds. "They are not controlling the environment like Afghanistan and Iraq. In Somalia, the situation is fluid, the situation is changing, personalities changing."

According to well-connected Somali sources, the CIA is reluctant to deal directly with Somali political leaders, who are regarded by US officials as corrupt and untrustworthy. Instead, the United States has Somali intelligence agents on its payroll. Somali sources with knowledge of the program described the agents as lining up to receive $200 monthly cash payments from Americans. "They support us in a big way financially," says the senior Somali intelligence official. "They are the largest [funder] by far."

According to former detainees, the underground prison, which is staffed by Somali guards, consists of a long corridor lined with filthy small cells infested with bedbugs and mosquitoes. One said that when he arrived in February, he saw two white men wearing military boots, combat trousers, gray tucked-in shirts and black sunglasses. The former prisoners described the cells as windowless and the air thick, moist and disgusting. Prisoners, they said, are not allowed outside. Many have developed rashes and scratch themselves incessantly. Some have been detained for a year or more. According to one former prisoner, inmates who had been there for long periods would pace around constantly, while others leaned against walls rocking.

A Somali who was arrested in Mogadishu and taken to the prison told The Nation that he was held in a windowless underground cell. Among the prisoners he met during his time there was a man who held a Western passport (he declined to identify the man's nationality). Some of the prisoners told him they were picked up in Nairobi and rendered on small aircraft to Mogadishu, where they were handed over to Somali intelligence agents. Once in custody, according to the senior Somali intelligence official and former prisoners, some detainees are freely interrogated by US and French agents. "Our goal is to please our partners, so we get more [out] of them, like any relationship," said the Somali intelligence official in describing the policy of allowing foreign agents, including from the CIA, to interrogate prisoners. The Americans, according to the Somali official, operate unilaterally in the country, while the French agents are embedded within the African Union force known as AMISOM.

Among the men believed to be held in the secret underground prison is Ahmed Abdullahi Hassan, a 25- or 26-year-old Kenyan citizen who disappeared from the congested Somali slum of Eastleigh in Nairobi around July 2009. After he went missing, Hassan's family retained Mbugua Mureithi, a well-known Kenyan human rights lawyer, who filed a habeas petition on his behalf. The Kenyan government responded that Hassan was not being held in Kenya and said it had no knowledge of his whereabouts. His fate remained a mystery until this spring, when another man who had been held in the Mogadishu prison contacted Clara Gutteridge, a veteran human rights investigator with the British legal organization Reprieve, and told her he had met Hassan in the prison. Hassan, he said, had told him how Kenyan police had knocked down his door, snatched him and taken him to a secret location in Nairobi. The next night, Hassan had said, he was rendered to Mogadishu.

According to the former fellow prisoner, Hassan told him that his captors took him to Wilson Airport: "'They put a bag on my head, Guantánamo style. They tied my hands behind my back and put me on a plane. In the early hours we landed in Mogadishu. The way I realized I was in Mogadishu was because of the smell of the sea — the runway is just next to the seashore. The plane lands and touches the sea. They took me to this prison, where I have been up to now. I have been here for one year, seven months. I have been interrogated so many times. Interrogated by Somali men and white men. Every day. New faces show up. They have nothing on me. I have never seen a lawyer, never seen an outsider. Only other prisoners, interrogators, guards. Here there is no court or tribunal.'"

After meeting the man who had spoken with Hassan in the underground prison, Gutteridge began working with Hassan's Kenyan lawyers to determine his whereabouts. She says he has never been charged or brought before a court. "Hassan's abduction from Nairobi and rendition to a secret prison in Somalia bears all the hallmarks of a classic US rendition operation," she says. The US official interviewed for this article denied the CIA had rendered Hassan but said, "The United States provided information which helped get Hassan — a dangerous terrorist — off the street." Human Rights Watch and Reprieve have documented that Kenyan security and intelligence forces have facilitated scores of renditions for the US and other governments, including eighty-five people rendered to Somalia in 2007 alone. Gutteridge says the director of the Mogadishu prison told one of her sources that Hassan had been targeted in Nairobi because of intelligence suggesting he was the "right-hand man" of Saleh Ali Saleh Nabhan, at the time a leader of Al Qaeda in East Africa. Nabhan, a Kenyan citizen of Yemeni descent, was among the top suspects sought for questioning by US authorities over his alleged role in the coordinated 2002 attacks on a tourist hotel and an Israeli aircraft in Mombasa, Kenya, and possible links to the 1998 US Embassy bombings in Kenya and Tanzania.

An intelligence report leaked by the Kenyan Anti-Terrorist Police Unit in October 2010 alleged that Hassan, a "former personal assistant to Nabhan…was injured while fighting near the presidential palace in Mogadishu in 2009." The authenticity of the report cannot be independently confirmed, though Hassan did have a leg amputated below the knee, according to his former fellow prisoner in Mogadishu.

Two months after Hassan was allegedly rendered to the secret Mogadishu prison, Nabhan, the man believed to be his Al Qaeda boss, was killed in the first known targeted killing operation in Somalia authorized by President Obama. On September 14, 2009, a team from the elite US counterterrorism force, the Joint Special Operations Command (JSOC), took off by helicopters from a US Navy ship off Somalia's coast and penetrated Somali airspace. In broad daylight, in an operation code-named Celestial Balance, they gunned down Nabhan's convoy from the air. JSOC troops then landed and collected at least two of the bodies, including Nabhan's.

Hassan's lawyers are preparing to file a habeas petition on his behalf in US courts. "Hassan's case suggests that the US may be involved in a decentralized, out-sourced Guantánamo Bay in central Mogadishu," his legal team asserted in a statement to The Nation. "Mr. Hassan must be given the opportunity to challenge both his rendition and continued detention as a matter of urgency. The US must urgently confirm exactly what has been done to Mr. Hassan, why he is being held, and when he will be given a fair hearing."

Gutteridge, who has worked extensively tracking the disappearances of terror suspects in Kenya, was deported from Kenya on May 11.

The underground prison where Hassan is allegedly being held is housed in the same building once occupied by Somalia's infamous National Security Service (NSS) during the military regime of Siad Barre, who ruled from 1969 to 1991. The former prisoner who met Hassan there said he saw an old NSS sign outside. During Barre's regime, the notorious basement prison and interrogation center, which sits behind the presidential palace in Mogadishu, was a staple of the state's apparatus of repression. It was referred to as Godka, "The Hole."

"The bunker is there, and that's where the intelligence agency does interrogate people," says Abdirahman "Aynte" Ali, a Somali analyst who has researched the Shabab and Somali security forces. "When CIA and other intelligence agencies — who actually are in Mogadishu — want to interrogate those people, they usually just do that." Somali officials "start the interrogation, but then foreign intelligence agencies eventually do their own interrogation as well, the Americans and the French." The US official said that US agents' "debriefing" prisoners in the facility has "been done on only rare occasions" and always jointly with Somali agents.

Some prisoners, like Hassan, were allegedly rendered from Nairobi, while in other cases, according to Aynte, "the US and other intelligence agencies have notified the Somali intelligence agency that some people, some suspects, people who have been in contact with the leadership of Al Shabab, are on their way to Mogadishu on a [commercial] plane, and to essentially be at the airport for those people. Catch them, interrogate them."

* * *

In the eighteen years since the infamous "Black Hawk Down" incident in Mogadishu, US policy on Somalia has been marked by neglect, miscalculation and failed attempts to use warlords to build indigenous counterterrorism capacity, many of which have backfired dramatically. At times, largely because of abuses committed by Somali militias the CIA has supported, US policy has strengthened the hand of the very groups it purports to oppose and inadvertently aided the rise of militant groups, including the Shabab. Many Somalis viewed the Islamic movement known as the Islamic Courts Union, which defeated the CIA's warlords in Mogadishu in 2006, as a stabilizing, albeit ruthless, force. The ICU was dismantled in a US-backed Ethiopian invasion in 2007. Over the years, a series of weak Somali administrations have been recognized by the United States and other powers as Somalia's legitimate government. Ironically, its current president is a former leader of the ICU.

Today, Somali government forces control roughly thirty square miles of territory in Mogadishu thanks in large part to the US-funded and -armed 9,000-member AMISOM force. Much of the rest of the city is under the control of the Shabab or warlords. Outgunned, the Shabab has increasingly relied on the linchpins of asymmetric warfare — suicide bombings, roadside bombs and targeted assassinations. The militant group has repeatedly shown that it can strike deep in the heart of its enemies' territory. On June 9, in one of its most spectacular suicide attacks to date, the Shabab assassinated the Somali government's minister of interior affairs and national security, Abdishakur Sheikh Hassan Farah, who was attacked in his residence by his niece. The girl, whom the minister was putting through university, blew herself up and fatally wounded her uncle. He died hours later in the hospital. Farah was the fifth Somali minister killed by the Shabab in the past two years and the seventeenth official assassinated since 2006. Among the suicide bombers the Shabab has deployed were at least three US citizens of Somali descent; at least seven other Americans have died fighting alongside the Shabab, a fact that has not gone unnoticed in Washington or Mogadishu.

During his confirmation hearings in June to become the head of the US Special Operations Command, Vice Admiral William McRaven said, "From my standpoint as a former JSOC commander, I can tell you we were looking very hard" at Somalia. McRaven said that in order to expand successful "kinetic strikes" there, the United States will have to increase its use of drones as well as on-the-ground intelligence, surveillance and reconnaissance operations. "Any expansion of manpower is going to have to come with a commensurate expansion of the enablers," McRaven declared. The expanding US counterterrorism program in Mogadishu appears to be part of that effort.

In an interview with The Nation in Mogadishu, Abdulkadir Moallin Noor, the minister of state for the presidency, confirmed that US agents "are working with our intelligence" and "giving them training." Regarding the US counterterrorism effort, Noor said bluntly, "We need more; otherwise, the terrorists will take over the country."

It is unclear how much control, if any, Somalia's internationally recognized president, Sheikh Sharif Sheikh Ahmed, has over this counterterrorism force or if he is even fully briefed on its operations. The CIA personnel and other US intelligence agents "do not bother to be in touch with the political leadership of the country. And that says a lot about the intentions," says Aynte. "Essentially, the CIA seems to be operating, doing the foreign policy of the United States. You should have had State Department people doing foreign policy, but the CIA seems to be doing it across the country."

While the Somali officials interviewed for this story said the CIA is the lead US agency on the Mogadishu counterterrorism program, they also indicated that US military intelligence agents are at times involved. When asked if they are from JSOC or the Defense Intelligence Agency, the senior Somali intelligence official responded, "We don't know. They don't tell us."

In April Ahmed Abdulkadir Warsame, a Somali man the United States alleged had links to the Shabab, was captured by JSOC forces in the Gulf of Aden. He was held incommunicado on a US Navy vessel for more than two months; in July he was transferred to New York and indicted on terrorism charges. Warsame's case ignited a legal debate over the Obama administration's policies on capturing and detaining terror suspects, particularly in light of the widening counterterrorism campaigns in Somalia and Yemen.

On June 23 the United States reportedly carried out a drone strike against alleged Shabab members near Kismayo, 300 miles from the Somali capital. As with the Nabhan operation, a JSOC team swooped in on helicopters and reportedly snatched the bodies of those killed and wounded. The men were taken to an undisclosed location. On July 6 three more US strikes reportedly targeted Shabab training camps in the same area. Somali analysts warned that if the US bombings cause civilian deaths, as they have in the past, they could increase support for the Shabab. Asked in an interview with The Nation in Mogadishu if US drone strikes strengthen or weaken his government, President Sharif replied, "Both at the same time. For our sovereignty, it's not good to attack a sovereign country. That's the negative part. The positive part is you're targeting individuals who are criminals."

A week after the June 23 strike, President Obama's chief counterterrorism adviser, John Brennan, described an emerging US strategy that would focus not on "deploying large armies abroad but delivering targeted, surgical pressure to the groups that threaten us." Brennan singled out the Shabab, saying, "From the territory it controls in Somalia, Al Shabab continues to call for strikes against the United States," adding, "We cannot and we will not let down our guard. We will continue to pummel Al Qaeda and its ilk."

While the United States appears to be ratcheting up both its rhetoric and its drone strikes against the Shabab, it has thus far been able to strike only in rural areas outside Mogadishu. These operations have been isolated and infrequent, and Somali analysts say they have failed to disrupt the Shabab's core leadership, particularly in Mogadishu.

In a series of interviews in Mogadishu, several of the country's recognized leaders, including President Sharif, called on the US government to quickly and dramatically increase its assistance to the Somali military in the form of training, equipment and weapons. Moreover, they argue that without viable civilian institutions, Somalia will remain ripe for terrorist groups that can further destabilize not only Somalia but the region. "I believe that the US should help the Somalis to establish a government that protects civilians and its people," Sharif said.

In the battle against the Shabab, the United States does not, in fact, appear to have cast its lot with the Somali government. The emerging US strategy on Somalia — borne out in stated policy, expanded covert presence and funding plans — is two-pronged: On the one hand, the CIA is training, paying and at times directing Somali intelligence agents who are not firmly under the control of the Somali government, while JSOC conducts unilateral strikes without the prior knowledge of the government; on the other, the Pentagon is increasing its support for and arming of the counterterrorism operations of non-Somali African military forces.

A draft of a defense spending bill approved in late June by the Senate Armed Services Committee would authorize more than $75 million in US counterterrorism assistance aimed at fighting the Shabab and Al Qaeda in Somalia. The bill, however, did not authorize additional funding for Somalia's military, as the country's leaders have repeatedly asked. Instead, the aid package would dramatically increase US arming and financing of AMISOM's forces, particularly from Uganda and Burundi, as well as the militaries of Djibouti, Kenya and Ethiopia. The Somali military, the committee asserted, is unable to "exercise control of its territory."

That makes it all the more ironic that perhaps the greatest tactical victory won in recent years in Somalia was delivered not by AMISOM, the CIA or JSOC but by members of a Somali militia fighting as part of the government's chaotic local military. And it was a pure accident.

Late in the evening on June 7, a man whose South African passport identified him as Daniel Robinson was in the passenger seat of a Toyota SUV driving on the outskirts of Mogadishu when his driver, a Kenyan national, missed a turn and headed straight toward a checkpoint manned by Somali forces. A firefight broke out, and the two men inside the car were killed. The Somali forces promptly looted the laptops, cellphones, documents, weapons and $40,000 in cash they found in the car, according to the senior Somali intelligence official.

Upon discovering that the men were foreigners, the Somali NSA launched an investigation and recovered the items that had been looted. "There was a lot of English and Arabic stuff, papers," recalls the Somali intelligence official, containing "very tactical stuff" that appeared to be linked to Al Qaeda, including "two senior people communicating." The Somali agents "realized it was an important man" and informed the CIA in Mogadishu. The men's bodies were taken to the NSA. The Americans took DNA samples and fingerprints and flew them to Nairobi for processing.

Within hours, the United States confirmed that Robinson was in fact Fazul Abdullah Mohammed, a top leader of Al Qaeda in East Africa and its chief liaison with the Shabab. Fazul, a twenty-year veteran of Al Qaeda, had been indicted by the United States for his alleged role in the 1998 US Embassy bombings and was on the FBI's "Most Wanted Terrorists" list. A JSOC attempt to kill him in a January 2007 airstrike resulted in the deaths of at least seventy nomads in rural Somalia, and he had been underground ever since. Secretary of State Hillary Clinton called Fazul's death "a significant blow to Al Qaeda, its extremist allies and its operations in East Africa. It is a just end for a terrorist who brought so much death and pain to so many innocents."

At its facilities in Mogadishu, the CIA and its Somali NSA agents continue to pore over the materials recovered from Fazul's car, which served as a mobile headquarters. Some deleted and encrypted files were recovered and decoded by US agents. The senior Somali intelligence official said that the intelligence may prove more valuable on a tactical level than the cache found in Osama bin Laden's house in Pakistan, especially in light of the increasing US focus on East Africa. The Americans, he said, were "unbelievably grateful"; he hopes it means they will take Somalia's forces more seriously and provide more support.

But the United States continues to wage its campaign against the Shabab primarily by funding the AMISOM forces, which are not conducting their mission with anything resembling surgical precision. Instead, over the past several months the AMISOM forces in Mogadishu have waged a merciless campaign of indiscriminate shelling of Shabab areas, some of which are heavily populated by civilians. While AMISOM regularly puts out press releases boasting of gains against the Shabab and the retaking of territory, the reality paints a far more complicated picture.

Throughout the areas AMISOM has retaken is a honeycomb of underground tunnels once used by Shabab fighters to move from building to building. By some accounts, the tunnels stretch continuously for miles. Leftover food, blankets and ammo cartridges lay scattered near "pop-up" positions once used by Shabab snipers and guarded by sandbags — all that remain of guerrilla warfare positions. Not only have the Shabab fighters been cleared from the aboveground areas; the civilians that once resided there have been cleared too. On several occasions in late June, AMISOM forces fired artillery from their airport base at the Bakaara market, where whole neighborhoods are totally abandoned. Houses lie in ruins and animals wander aimlessly, chewing trash. In some areas, bodies have been hastily buried in trenches with dirt barely masking the remains. On the side of the road in one former Shabab neighborhood, a decapitated corpse lay just meters from a new government checkpoint.

In late June the Pentagon approved plans to send $45 million worth of military equipment to Uganda and Burundi, the two major forces in the AMISOM operation. Among the new items are four small Raven surveillance drones, night-vision and communications equipment and other surveillance gear, all of which augur a more targeted campaign. Combined with the attempt to build an indigenous counterterrorism force at the Somali NSA, a new US counterterrorism strategy is emerging.

But according to the senior Somali intelligence official, who works directly with the US agents, the CIA-led program in Mogadishu has brought few tangible gains. "So far what we have not seen is the results in terms of the capacity of the [Somali] agency," says the official. He conceded that neither US nor Somali forces have been able to conduct a single successful targeted mission in the Shabab's areas in the capital. In late 2010, according to the official, US-trained Somali agents conducted an operation in a Shabab area that failed terribly and resulted in several of them being killed. "There was an attempt, but it was a haphazard one," he recalls. They have not tried another targeted operation in Shabab-controlled territory since.

The Journalism Fellowship Program enables and supports prominent journalists to write on complex social and political issues facing America and the world. Our Fellows form a unique community of thinkers and writers, and are energetic contributors to the intellectual life of the country. We also encourage our Fellows to pursue book projects, write Op-Eds and appear as commentators, critics or analysts on radio and television.

The Nation Institute currently has two endowed fellowships, the Puffin and the Knobler Fellowships. If you want to learn more about our named fellowship programs, or if you wish to endow a fellowship, please contact Executive Director Taya Kitman at 212-822-0252 or taya@nationinstitute.org.

A nonprofit media center, The Nation Institute is dedicated to strengthening the independent press and advancing social justice and civil rights. Our dynamic range of programs includes a bestselling book publishing imprint, Nation Books; our award-winning Investigative Fund, which supports groundbreaking investigative journalism; the widely read and syndicated website TomDispatch; the Victor S. Navasky Internship Program at The Nation magazine; and Journalism Fellowships that fund over 20 high-profile reporters every year.

All of our work is made possible by the generous support of individuals and institutions committed to a free and independent press, civil liberties and social justice. The Institute is a 501(c) (3) public foundation, donations to which are tax deductible to the fullest extent provided by law. If you have any questions, or would like other donation options, visit our donate page or contact us at (212) 822-0252.

If contributing by mail, make your check payable to "The Nation Institute" and send to: